Chancellor Carmen Fariña mounted a strong defense Wednesday of Michael Wiltshire, the veteran principal tapped to transform struggling Boys and Girls High School in Brooklyn, after it was revealed that he is considering leaving the school.

Wiltshire has recently run into challenges at Boys and Girls and another school he oversees, Medgar Evers College Preparatory School, where he is the subject of an ongoing city investigation, officials confirmed Wednesday. Chalkbeat reported Tuesday that Wiltshire has interviewed for the principalship of suburban Uniondale High School on Long Island but has not decided whether to accept it.

On Wednesday, the community education council in Boys and Girls’ Bedford-Stuyvesant district announced a public meeting next week to discuss “alarming concerns surrounding the future” of that school. The meeting will address parents’ complaints about Wiltshire dividing his time between two schools and a lack of information from the education department about its plans for the school, the council president said.

Wiltshire’s departure would complicate the city’s turnaround efforts at one of its lowest performing schools, and would also throw into question the direction of Medgar Evers — the selective school Wiltshire also oversees as “master principal.” Asked whether she was rethinking that plan on Wednesday, Fariña said she “absolutely” stood by her decision to let Wiltshire run the two schools simultaneously.

Fariña noted that Wiltshire has improved Boys and Girls’ graduation rate since taking over in October 2014: 50 percent of students graduated on time last year, compared to 42 percent of students the previous year. However, the school’s enrollment has dropped by half during that time, and some of the school’s lowest-performing students were urged to switch schools soon after Wiltshire arrived at Boys and Girls.

“I think he’s done a great job stabilizing the building, making sure that more students are on their way to graduation,” Fariña said during an unrelated press conference.

She said that Wiltshire planned to remain at both schools at least through the end of June, and downplayed the impact of his potential departure. “Every year principals leave for other jobs or want to rethink their jobs,” Fariña said.

Under Wiltshire, long-struggling but historic Boys and Girls has also seen its student and teacher attendance rates improve and its suspension rate fall by nearly 60 percent. Fariña also praised his performance during a City Council hearing last week.

Still, Wiltshire has encountered difficulties recently at both of his schools.

Angella Smith, a Medgar Evers assistant principal who was helping run the school when Wiltshire was away, was removed due to an investigation involving her, forcing Wiltshire to spend more time at the school. Wiltshire is involved in a separate investigation relating to a matter at Medgar Evers, a spokeswoman for the city’s special commissioner of investigation said Wednesday.

Meanwhile, a nonprofit that provides social services at Boys and Girls announced plans last week to pull out of the school after repeatedly clashing with Wiltshire, and the leadership team at Medgar Evers rejected his plan to move that school into Boys and Girls’ campus. And on Tuesday, some parents and students at Medgar Evers held a rally to protest the city’s appointment of a separate principal, Angello Marra, to help run that school for the next few weeks.

NeQuan McLean, president of the District 16 community education council, said the meeting scheduled for Monday morning is meant to bring together local residents and politicians who are troubled by the recent news about Boys and Girls and want more information from the city.

“This is supposed to be a community school, and the community isn’t aware of anything that’s going on at the school,” he said. “That’s a problem.”

Education department spokeswoman Devora Kaye said the city has held several meetings with the council and community members about the plan to move Medgar Evers, and council leaders took part in a tour of Boys and Girls’ campus before the move was officially proposed. She added that department officials would take part in Monday’s meeting, and “will continue to have ongoing conversations with them and the greater school community about these important issues.”

Alex Zimmerman contributed reporting.